Galli Mary, Feng Fan, Gallavotti Andrea
Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ, United States.
Department of Plant Biology, Rutgers University, New Brunswick, NJ, United States.
Front Genet. 2020 Oct 28;11:591194. doi: 10.3389/fgene.2020.591194. eCollection 2020.
The domestication and improvement of many plant species have frequently involved modulation of transcriptional outputs and continue to offer much promise for targeted trait engineering. The cis-regulatory elements (CREs) controlling these trait-associated transcriptional variants however reside within non-coding regions that are currently poorly annotated in most plant species. This is particularly true in large crop genomes where regulatory regions constitute only a small fraction of the total genomic space. Furthermore, relatively little is known about how CREs function to modulate transcription in plants. Therefore understanding where regulatory regions are located within a genome, what genes they control, and how they are structured are important factors that could be used to guide both traditional and synthetic plant breeding efforts. Here, we describe classic examples of regulatory instances as well as recent advances in plant regulatory genomics. We highlight valuable molecular tools that are enabling large-scale identification of CREs and offering unprecedented insight into how genes are regulated in diverse plant species. We focus on chromatin environment, transcription factor (TF) binding, the role of transposable elements, and the association between regulatory regions and target genes.
许多植物物种的驯化和改良常常涉及转录输出的调控，并且在靶向性状工程方面仍有很大潜力。然而，控制这些与性状相关的转录变体的顺式调控元件（CRE）位于非编码区域，目前在大多数植物物种中注释很少。在大型作物基因组中尤其如此，其中调控区域仅占总基因组空间的一小部分。此外，关于CRE如何在植物中调节转录的了解相对较少。因此，了解调控区域在基因组中的位置、它们控制哪些基因以及它们的结构如何，是可用于指导传统和合成植物育种工作的重要因素。在这里，我们描述了调控实例的经典例子以及植物调控基因组学的最新进展。我们强调了有价值的分子工具，这些工具能够大规模鉴定CRE，并为不同植物物种中基因的调控方式提供前所未有的见解。我们关注染色质环境、转录因子（TF）结合、转座元件的作用以及调控区域与靶基因之间的关联。
